Contacts of the helix formed by residues 352 - 373 (chain C) in PDB entry 6E7P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 352 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 3.6 28.4 + - - +
49C PHE* 5.6 3.4 - - - -
319C SER* 4.9 2.4 + - - -
320C LEU* 5.3 1.8 - - - +
349C GLU 5.0 4.4 + - - -
350C PHE 3.3 9.4 + - - -
351C VAL* 1.3 80.4 - - - +
353C GLY* 1.3 64.9 + - - +
354C TRP* 4.4 7.2 - - + +
355C TYR* 3.3 46.1 + - + +
356C ILE* 3.7 8.1 + - - +
403C ARG* 6.3 0.2 - - - -
801C HZ7 5.1 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 353 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351C VAL 3.5 4.5 + - - -
352C ASN* 1.3 70.5 - - - +
354C TRP* 1.3 68.7 + - - +
356C ILE* 3.4 24.5 - - - +
357C LEU* 3.6 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 354 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352C ASN* 3.2 5.7 - - + -
353C GLY* 1.3 82.0 - - - +
355C TYR* 1.3 65.2 + - + +
357C LEU* 3.5 20.7 + - + +
358C LEU* 3.1 28.7 + - + +
399C VAL* 3.9 20.4 - - + -
400C GLY* 4.4 8.7 - - - -
402C ILE* 4.4 14.1 - - + -
403C ARG* 3.9 66.8 - - + +
406C THR* 5.3 9.4 + - + -
415C ILE* 5.7 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 355 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 6.1 0.3 - - - +
315C LEU* 6.1 1.8 - - + -
316C CYS* 3.9 41.3 - - + +
319C SER* 4.6 10.5 - - - -
320C LEU* 4.3 19.3 - - + -
352C ASN* 3.3 39.2 + - + +
354C TRP* 1.3 76.3 - - - +
356C ILE* 1.3 60.0 + - - +
358C LEU* 3.0 9.5 + - + +
359C VAL* 2.8 34.1 + - - +
403C ARG* 3.3 40.9 + - - -
801C HZ7 2.5 42.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 356 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320C LEU* 4.6 18.5 - - + +
351C VAL* 5.4 6.1 - - + -
352C ASN 3.7 4.3 + - - +
353C GLY* 3.4 23.3 - - - +
355C TYR* 1.3 77.4 - - - +
357C LEU* 1.3 54.1 + - - +
359C VAL* 3.8 18.1 - - + +
360C THR* 2.3 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 357 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353C GLY 3.8 9.2 - - - +
354C TRP* 3.5 24.0 + - + +
355C TYR 3.1 0.4 - - - -
356C ILE* 1.3 83.5 - - + +
358C LEU* 1.3 71.9 + - + +
360C THR* 3.3 13.1 + - - -
361C SER* 3.3 11.6 + - - -
396C LEU* 3.3 56.8 - - + +
399C VAL* 4.3 15.5 - - + -
400C GLY* 4.6 9.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 358 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLN* 3.4 49.1 - - + +
72C LYS* 3.8 4.1 + - - +
316C CYS* 4.7 16.2 - - - -
354C TRP* 3.1 18.5 + - + +
355C TYR* 3.0 14.1 + - + +
357C LEU* 1.3 85.2 - - + +
359C VAL* 1.3 63.6 + - - +
361C SER* 3.3 14.7 + - - +
362C ASP* 3.0 23.1 - - - +
396C LEU 5.5 1.3 - - - +
397C VAL* 5.4 7.4 - - + +
400C GLY* 5.2 10.5 - - - -
403C ARG* 4.6 16.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 359 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C PHE* 3.6 31.8 - - + +
316C CYS* 4.6 15.3 - - + -
317C ALA* 4.8 5.8 - - + +
320C LEU* 3.7 26.5 - - + -
355C TYR 2.8 19.2 + - - +
356C ILE* 3.8 17.3 - - + +
357C LEU 3.3 0.4 - - - -
358C LEU* 1.3 76.9 - - - +
360C THR* 1.3 63.9 + - - +
362C ASP* 3.4 4.2 + - - +
363C VAL* 3.1 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 360 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356C ILE* 2.3 31.0 + - - +
357C LEU* 3.3 11.0 + - - -
359C VAL* 1.3 78.3 - - - +
361C SER* 1.3 62.3 + - - +
363C VAL* 3.3 6.8 + - - +
364C LEU* 3.2 39.9 + - + +
396C LEU* 4.4 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 361 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LYS* 4.2 3.5 + - - -
357C LEU 3.3 4.8 + - - -
358C LEU* 3.3 15.1 + - - +
360C THR* 1.3 79.4 - - - +
362C ASP* 1.3 58.7 + - - +
364C LEU* 2.8 9.9 + - - +
365C THR* 2.5 42.9 + - - -
393C SER* 4.4 7.4 - - - +
396C LEU* 3.7 21.5 - - - +
397C VAL* 3.8 28.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 362 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LYS* 2.7 40.8 + - - +
309C CYS* 3.4 39.7 - - + +
312C SER* 3.7 7.1 + - - +
313C PHE* 3.9 21.6 + - + +
316C CYS* 5.6 0.3 - - - +
358C LEU* 3.0 12.9 + - - +
359C VAL* 3.4 4.4 + - - +
360C THR 3.3 0.8 - - - -
361C SER* 1.3 79.6 + - - +
363C VAL* 1.3 65.1 + - - +
365C THR* 3.9 5.4 + - - +
366C ILE* 3.3 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 363 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C PHE* 4.1 20.0 - - + -
359C VAL* 3.1 20.5 + - + +
360C THR* 3.5 9.9 - - + +
362C ASP* 1.3 76.4 - - - +
364C LEU* 1.3 70.7 + - + +
366C ILE* 4.1 3.9 - - - +
367C SER* 3.2 26.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 364 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C THR* 3.2 31.2 + - + +
361C SER* 2.8 11.0 + - - +
363C VAL* 1.3 86.8 - - + +
365C THR* 1.3 56.3 + - - +
367C SER* 3.4 5.6 + - - -
368C GLY* 2.6 33.4 + - - -
389C LEU* 4.1 45.9 - - + +
392C THR* 4.2 25.4 - - + -
393C SER* 4.5 5.8 - - - +
396C LEU* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 365 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C VAL* 4.3 15.8 - - + +
305C VAL* 4.0 15.9 - - + -
309C CYS* 3.7 29.3 - - - -
361C SER* 2.5 30.8 + - - -
362C ASP* 4.3 3.7 + - - -
364C LEU* 1.3 72.6 - - - +
366C ILE* 1.3 59.0 + - - +
368C GLY* 3.0 1.6 + - - -
369C THR* 2.9 35.6 + - + +
390C LEU* 4.5 5.3 - - + +
393C SER* 3.3 22.5 - - - +
397C VAL* 5.0 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 366 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C VAL 4.9 1.1 - - - +
306C ILE* 3.5 52.9 - - + +
309C CYS* 5.1 7.6 - - + +
310C SER* 4.0 19.1 - - - +
362C ASP 3.3 18.6 + - - +
363C VAL* 4.1 4.3 - - - +
365C THR* 1.3 80.3 - - - +
367C SER* 1.3 61.6 + - - +
369C THR* 3.8 3.8 - - - -
370C ILE* 3.3 27.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 367 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C VAL* 3.2 22.7 + - - -
364C LEU* 3.7 6.1 - - - -
365C THR 3.2 0.4 - - - -
366C ILE* 1.3 79.1 - - - +
368C GLY* 1.3 64.7 + - - +
370C ILE* 3.3 18.7 - - - +
371C MET* 3.6 13.3 + - - +
389C LEU* 4.0 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 368 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C LEU 2.6 21.7 + - - -
365C THR 3.0 2.2 + - - -
367C SER* 1.3 72.9 - - - +
369C THR* 1.3 58.7 + - - +
371C MET* 2.9 22.2 + - - +
372C LYS* 3.0 10.9 + - - +
386C CYS 4.8 3.0 - - - +
389C LEU* 4.1 20.4 - - - -
390C LEU* 4.1 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 369 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLN* 3.9 20.2 - - + +
302C ASP* 4.6 14.8 - - - +
305C VAL* 3.8 28.0 - - + +
306C ILE* 4.4 12.4 - - - +
365C THR* 2.9 22.5 + - + +
366C ILE* 3.8 8.7 + - - +
368C GLY* 1.3 71.8 - - - +
370C ILE* 1.3 61.4 + - - +
372C LYS* 3.2 18.5 + - - +
373C ILE* 3.3 19.4 + - - +
390C LEU* 3.8 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 370 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C ILE* 5.8 6.9 - - + +
366C ILE* 3.3 24.1 + - + +
367C SER* 3.3 14.6 - - - +
369C THR* 1.3 80.3 + - - +
371C MET* 1.3 64.2 + - + +
372C LYS 3.4 0.2 - - - -
373C ILE* 3.6 30.2 - - + +
374C GLY 4.5 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 371 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C SER* 3.8 11.7 - - - +
368C GLY* 2.9 10.8 + - - +
370C ILE* 1.3 79.5 - - + +
372C LYS* 1.3 60.1 + - - +
373C ILE 3.2 2.2 - - - -
374C GLY* 3.1 21.8 + - - +
380C LEU* 4.2 26.1 - - + +
382C SER* 5.3 7.6 - - - +
385C VAL* 4.8 15.7 - - + -
386C CYS* 3.7 31.5 - - + +
389C LEU* 5.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 372 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLN* 3.4 33.3 + - - +
82C LEU 5.8 1.4 + - - -
83C PHE* 3.8 41.7 - - + +
298C ARG* 4.3 36.3 + - - +
302C ASP* 4.8 14.5 + - + +
368C GLY 3.0 11.3 + - - +
369C THR* 3.2 15.9 + - - +
371C MET* 1.3 75.5 - - - +
373C ILE* 1.3 62.0 + - - +
374C GLY 3.1 1.6 + - - -
375C ILE* 3.8 24.7 + - - +
386C CYS* 4.6 7.8 - - + +
390C LEU* 4.5 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 373 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ASP* 3.6 19.1 - - - +
306C ILE* 4.5 17.3 - - + -
369C THR 3.3 16.6 - - - +
370C ILE* 3.6 28.5 - - + +
371C MET 3.2 0.2 - - - -
372C LYS* 1.3 78.3 - - - +
374C GLY* 1.3 50.3 + - - +
375C ILE* 2.7 17.2 + - - +
376C GLU* 3.6 12.4 + - - +
377C ALA 5.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il